Using our allele-specific PCR assay, which allows detection and quantification of rare mutations at levels as low as 0.1% in a virus population, we are performing studies designed to understand the dynamics of appearance and disappearance of NNRTI resistance mutations in patients starting and stopping therapy as well as in drug-naive patients. In collaboration with Dr. John Mellors (University of Pittsburgh), we are assessing the impact of low-frequency mutations on subsequent treatment failure. In collaboration with Drs. Lynn Morris (National Institute for Communicable Diseases, South Africa) and Pat Robertson (Boehringer Ingelheim), we are also analyzing the rise and fall of NNRTI resistance mutations in women exposed to single-dose nevirapine to prevent mother-to-infant transmission, and to assess the consequences of these mutations for subsequent nevirapine-based therapy. The assay is also being used for collaborative studies with DRP investigators. With Dr. Vineet KewalRamani (National Cancer Institute), we are assessing the appearance of NNRTI resistance mutations in a pigtail macaque model of infection with SIV containing HIV RT (RT-SHIV) and treated with efavirenz, as a model for the evolution of resistance in humans so treated. In collaboration with Dr. Eric Freed (National Cancer Institute), we are developing a sensitive assay for the duplication of the PTAP motif in the p6 portion of Gag frequently found in association with drug resistance. An advanced version of the allele-specific PCR assay is currently under development to increase the sensitivity of mutant detection 10-100 fold. As a result, the new assay will approach detection of mutations occurring at a frequency that approximates the HIV-1 reverse transcriptase mutation rate. We will therefore be able to determine with great sensitivity the relative levels of drug resistance mutations present prior to drug initiation. These studies will be essential to understanding the relative level of pre-existing drug resistance that contributes to subsequent drug failure during antiretroviral therapy. We are also using this approach to investigate the impact of drug resistance mutations in HIV-1-infected populations over time. With Drs. H. Clifford Lane and R. Davey (NIAID), we are investigating the presence of drug resistance mutations in samples obtained relatively early in the epidemic (1988-1990) prior to the widespread introduction of antiretroviral therapy. As a result, we will be able to determine the relative prevalence of HIV-1 mutations in the absence of any potential effect of antiretroviral therapy. These studies will be particularly useful in understanding the role of drug resistance that is transmitted at the time of infection. Comparison of the relative level of drug resistance mutations in samples from patients from the pre-antiretroviral era with those obtained from contemporary drug-nave populations will offer new insights into the influence of transmitted drug resistance on the overall prevalence of drug resistance. [Corresponds to Project 3 in the April 2007 site visit report of the Host-Virus Interaction Branch, HIV Drug Resistance Program]